Journal: American Journal of Cancer Research

Article Title: Identification of DHX36 as a tumour suppressor through modulating the activities of the stress-associated proteins and cyclin-dependent kinases in breast cancer

doi:

Figure Lengend Snippet: Expression levels of DHX36 gene and protein are associated with the survival and clinicopathological features of breast cancer patients. The Kaplan-Meier survival curve was plotted using the pooled gene expression data from www.kmplot.com (Cut-off value: 1257.33. n=1764). A. OS. B. RFS. C. DHX36 gene expression is downregulated in the primary tumour as indicated by the analysis of The Cancer Genome Atlas-Breast invasive carcinoma (TCGA-BRCA) dataset (n=1211). D. Expression level of the DHX36 gene is lower in advanced stages (T3+T4) than in earlier stages (T1+T2) as indicated by the TCGA-BRCA data. E. Expression level of the DHX36 gene is higher in TNBC (n=123) than in non-TNBC (n=605) as indicated by the TCGA-BRCA data. Equivocal: The ER/PR/HER3 status is partially determined. NDA: No data available for the ER/PR/HER3 status. F. Frequency of DHX36 staining scores in different pathological types in breast cancer tissue arrays. G. Frequency of DHX36 staining scores in different stages in breast cancer tissue arrays. H. Kaplan-Meier survival analysis of the breast cancer tissue arrays following DHX36 staining by immunohistochemistry. Representative images of the differential staining intensity of DHX36 in normal breast and breast cancer tissues were shown in Supporting Information Figure S1. Clinicopathological status of the three tissue microarray slides was provided in Table 1.

Article Snippet: The profile of stress-associated kinase proteins indicated by the Kinex antibody microarray.

Techniques: Expressing, Gene Expression, Staining, Immunohistochemistry, Microarray

Journal: American Journal of Cancer Research

Article Title: Identification of DHX36 as a tumour suppressor through modulating the activities of the stress-associated proteins and cyclin-dependent kinases in breast cancer

doi:

Figure Lengend Snippet: The effect of DHX36 knockdown on signalling pathways of breast cancer cells. A. The profile of stress-associated kinase proteins indicated by the Kinex antibody microarray. B. The profile of mitotic checkpoint protein-serine kinases indicated by the Kinex antibody microarray. The change of protein level in the antibody microarray was calculated as %CFC = (SignalKD - SignalScr)/SignalScr*100 after global normalization. FACS analysis was conducted to evaluate the endogenous levels of JNK and phosphor-JNK (pJNK) proteins. C, D. Levels of total JNK protein in the stable BT549 cell lines with Scr control (left) and DHX36 shRNA (right). E, F. Levels of the phosphorylated JNK protein in the stable BT549 cell lines with Scr control (left) and DHX36 shRNA (right). G, H. Levels of total JNK protein in the stable MDA-MB-231 cell lines with Scr control (left) and DHX36 shRNA (right). I, J. Levels of the phosphorylated JNK protein in the stable MDA-MB-231 cell lines with Scr control (left) and DHX36 shRNA (right). K. Western blotting of the JNK and pJNK proteins in the breast cancer cell lines. L. Real-time qRT-PCR showing the gene expression level of JNK in the breast cancer lines.

Article Snippet: The profile of stress-associated kinase proteins indicated by the Kinex antibody microarray.

Techniques: Knockdown, Microarray, Control, shRNA, Western Blot, Quantitative RT-PCR, Gene Expression

Journal: Nature Communications

Article Title: A therapeutic antibody targeting osteoprotegerin attenuates severe experimental pulmonary arterial hypertension

doi: 10.1038/s41467-019-13139-9

Figure Lengend Snippet: OPG activates pro-proliferative signalling and a disease-relevant transcriptome. Panel ( a ) Signalling Pathway Impact Analysis (SPIA) with each pathway represented by one dot. The pathways to the right of the red diagonal line are significant after Bonferroni correction of the global p -values obtained using Fisher’s methods from the combination of pPERT and pNDE values, the pathways to the right of the blue line are significant after FDR correction. ( b ) shows a heat map of significant differentially regulated genes after gene enrichment against PAH-associated genes in OPG stimulated PASMCs, ( c ) TaqMan validation of gene expression microarray, TaqMan expression data normalised using ΔΔCT with 18 s rRNA as the endogenous control gene. Panel ( d ) shows a heat map of cell cycle/CDK proteins significantly regulated by OPG at 10 and 60 min expressed as a ratio to unstimulated controls from the same time point from Kinex phospho-arrays identified, with ( e ) showing those specifically related to NF-κβ. f Western blot validation of Kinex array data in unstimulated (0.2% FCS, Un) or OPG-stimulated (50 ng ml −1 ) PASMCs at 10 min (10) and 60 min (60) with relative band densities of phospho-ERK1/2, phospho-HSP27, phospho-mTOR, phospho-CDK4 and total CDK5 are shown by the bar graphs and representative western blot images shown above the graph. Heat maps show Z-ratio gene or protein expression. Bars represent mean with error bars showing the standard error of the mean, n = 3 for pooled triplicate samples ( a , b ), n = 12 ( c ), n = 4 ( d , e ), n = 5 ( f ) from three donors of PASMCs, dots represent experimental repeats. Bars from unstimulated cells are white, OPG stimulated blue. * p < 0.05, ** p < 0.01, *** p < 0.001 compared OPG-stimulated to unstimulated PASMCs using one-way ANOVA followed by Bonferroni’s multiple comparisons post hoc test. When there were only two groups, unpaired t-tests were used

Article Snippet: Cells were then stimulated with 0.2% (v/v) FBS (negative), rhOPG (50 ng ml −1 ) and PDGF (20 ng ml −1 ) for 10 and 60 min. Phosphorylation targets were identified from protein lysates by Kinex antibody microarray (Kinexus, Vancouver, Canada).

Techniques: Expressing, Microarray, Western Blot

Journal: eLife

Article Title: Inhibition of ErbB kinase signalling promotes resolution of neutrophilic inflammation

doi: 10.7554/eLife.50990

Figure Lengend Snippet: Kinexus antibody microarray analysis. Ultrapurified neutrophils were incubated with N 6 -MB-cAMP [100 µM] for 30 and 60 min or lysed immediately following isolation (0’). Lysates from four donors were pooled prior to Kinex antibody microarray analysis. Table shows all targets for which phospho-antibodies had Z ratios of >1.5 compared to t = 0 baseline control, at each timepoint. ErbB related antibodies are in bold.

Article Snippet: Lysates (containing protein at 6 mg/mL) from four donors were pooled prior to Kinex antibody microarray analysis (Kinexus Bioinformatics) ( ).

Techniques: Microarray, Incubation, Isolation

Journal: Oncotarget

Article Title: Distinct mechanisms by which two forms of miR-140 suppress the malignant properties of lung cancer cells

doi: 10.18632/oncotarget.26356

Figure Lengend Snippet: Association of RNA-Seq data after biotinylated-miRNA pull down with Kinex™ Antibody Microarray data from cells treated with miR-140-3p

Article Snippet: To explore the targeting and mechanisms of the miR-140 strands in a global manner, the pulldown gene targets by biotin-miRNA mimics were analysed by Ion Proton RNA sequencing, which were integrated with the proteomic profile from Kinex™ Antibody Microarray with 878 antibodies embedded.

Techniques: Microarray, In Silico

Journal: Oncotarget

Article Title: Distinct mechanisms by which two forms of miR-140 suppress the malignant properties of lung cancer cells

doi: 10.18632/oncotarget.26356

Figure Lengend Snippet: Association of RNA-Seq data after biotinylated-miRNA pull down with Kinex™ Antibody Microarray data from cells treated with miR-140-5p

Article Snippet: To explore the targeting and mechanisms of the miR-140 strands in a global manner, the pulldown gene targets by biotin-miRNA mimics were analysed by Ion Proton RNA sequencing, which were integrated with the proteomic profile from Kinex™ Antibody Microarray with 878 antibodies embedded.

Techniques: Microarray, In Silico